The company blamed the shortfall on delays from some financial institutions in signing licensing deals for Mitek’s mobile deposit technology, which is used by financial institutions ranging from Chase to San Diego County Credit Union.

“Mitek reported a somewhat disastrous second quarter, with revenue of $1.2 million, well below consensus estimates of $4.5 million,” said William Blair analyst Bhavan Suri in a research report.

The company lost $2.2 million, or 9 cents a share, excluding certain charges. Analysts expected a loss of 3 cents per share.

Suri said the poor results were “very surprising” given that more than 300 financial institutions have agreed to use Mitek’s technology for their mobile deposit services.

But Jim Debello, Mitek’s chief executive, said in a conference call that only 100 of those 300 banks and credit unions have actually begun offering Mitek powered mobile deposits apps to their customers.

“This is an emerging market,” he said. “These are new (clients) that are beginning to launch these products to their customers. It takes time.”

DeBello denied that financial institutions were putting off signing licenses because of concerns over Mitek’s patent lawsuit with financial services giant USAA.

Mitek and USAA sued each other last month in federal court over which firm created mobile deposit technology.

“While the lawsuit has required management’s time, we strongly believe in our intellectual property position and we are confident that we will prevail,” DeBello said. “Our customers have been extremely supportive and remain undeterred in supporting their commercial launches of mobile deposit.”

Mitek’s shares fell $3.25 Thursday to end the day at $2.53 on the Nasdaq. The stock is down nearly 65 percent so far this year.

The company’s imaging technology allows smartphone users to snap pictures of checks and use the app to submit them for deposit.

Suri, the William Blair analyst, expects Mitek’s financial results to remain volatile in the short run. But he’s more optimistic over the long haul.

“We view mobile check deposit as an application that is easily understood and accepted by consumers and fosters the use of mobile apps for banking, supporting our thesis that banks view mobile deposit as a customer-acquisition strategy,” he said.